Simplifying Blender's UI
Before coding your own custom version of blender, start with what blender already offers -


Maximise Area makes the current editor (usually the 3D view) take up the entire window area while leaving the Info Bar at the top and viewport headers visible. In 2.7x press &#9096; Ctrl&#8593; Up arrow, in 2.80 press &#9096; CtrlSpace
Fullscreen Area makes the current editor take up the entire window without the info bar or headers being visible. In 2.7x press &#9095; AltF10, in 2.80 press &#9096; Ctrl&#9095; AltSpace
Screens are preset window layouts that we can easily switch between, in 2.80 these are replaced with workspaces. If any of the included screens do not suit your requirements you can create your own or adjust the included screens. By setting up screens and saving them in your startup blend file, you can have them each time you use blender. This means you can manually setup a layout the way you want and always have it available and active when you first start blender. Note that you may want to disable the Load UI option to prevent other peoples screens being loaded when you open a blend file.


By making the 3D view full screen you still have the tool shelf and properties regions. You can use python to define your own custom panel to make specific things/actions easily available to you and by putting it in an addon it can always be there. You may also want to get creative and misuse the ability to alter header contents with an addon, say you never use the VSE, then you can setup a screen that has a small VSE area available that shows buttons or menus that you define.